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- PDB-8pjw: Crystal structure of the computationally designed SAKe6FE protein -

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Basic information

Entry
Database: PDB / ID: 8pjw
TitleCrystal structure of the computationally designed SAKe6FE protein
ComponentsSAKe6FE
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWouters, S.M.L.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S89918N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: To Be Published
Title: Computational design of the SAKe scaffold proteins
Authors: Wouters, S.M.L. / Noguchi, H. / Voet, A.R.D.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAKe6FE
B: SAKe6FE


Theoretical massNumber of molelcules
Total (without water)61,9192
Polymers61,9192
Non-polymers00
Water6,702372
1
A: SAKe6FE


Theoretical massNumber of molelcules
Total (without water)30,9601
Polymers30,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAKe6FE


Theoretical massNumber of molelcules
Total (without water)30,9601
Polymers30,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.703, 65.603, 78.283
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein SAKe6FE


Mass: 30959.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M AmSO4 , 0.1 M Na acetate pH 4.6, 30%(w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→39.74 Å / Num. obs: 55648 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.17 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.047 / Rrim(I) all: 0.112 / Net I/σ(I): 10.6 / Num. measured all: 300640
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.708 / Num. measured all: 14862 / Num. unique obs: 2764 / CC1/2: 0.798 / Rpim(I) all: 0.336 / Rrim(I) all: 0.786 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→33.65 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 2740 4.93 %
Rwork0.1764 52877 -
obs0.1778 55617 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.45 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 0 372 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244364
X-RAY DIFFRACTIONf_angle_d1.55245977
X-RAY DIFFRACTIONf_chiral_restr0.3521658
X-RAY DIFFRACTIONf_plane_restr0.0147785
X-RAY DIFFRACTIONf_dihedral_angle_d20.70871460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.36921350.29112650X-RAY DIFFRACTION99.82
1.68-1.710.3021400.26192608X-RAY DIFFRACTION99.75
1.71-1.740.29781280.24662636X-RAY DIFFRACTION99.68
1.74-1.780.28641470.22422625X-RAY DIFFRACTION99.75
1.78-1.820.26971320.19942632X-RAY DIFFRACTION99.68
1.82-1.860.2361300.18272635X-RAY DIFFRACTION99.93
1.86-1.90.22961580.17952651X-RAY DIFFRACTION99.89
1.9-1.960.19251540.17092597X-RAY DIFFRACTION99.89
1.96-2.010.2251240.16842622X-RAY DIFFRACTION100
2.01-2.080.20411210.16742681X-RAY DIFFRACTION99.93
2.08-2.150.21430.17132611X-RAY DIFFRACTION99.93
2.15-2.240.21321230.17862667X-RAY DIFFRACTION100
2.24-2.340.2081230.17332657X-RAY DIFFRACTION99.75
2.34-2.460.22351410.18892628X-RAY DIFFRACTION99.86
2.46-2.620.19421220.18792695X-RAY DIFFRACTION99.93
2.62-2.820.22841350.1892635X-RAY DIFFRACTION99.86
2.82-3.10.1771420.17452638X-RAY DIFFRACTION99.86
3.1-3.550.1861520.16182637X-RAY DIFFRACTION99.08
3.55-4.470.1461260.13842686X-RAY DIFFRACTION99.72
4.48-33.650.1861640.17022686X-RAY DIFFRACTION99.34

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